Computational protocol: Isolation of midgut escape mutants of two American genotype dengue 2 viruses from Aedes aegypti

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Protocol publication

[…] DENV2 strains included in the phylogenetic analysis have the following NCBI GenBank accession numbers: D2/PF/UH50/1972 (HM582108.1), D2/PF/UH57/1971 (HM582109), D2/FJ/UH21/1971 (HM582099), D2/FJ/UH22/1971 (HM582101.1), D2/FJ/UH40/1971 (HM582100.1), D2/NC/UH37/1971 (HM582102.1), D2/NC/UH97/1972 (HM582103.1), D2/TO/UH00/1973 (HM582110), D2/TO/UH04/1974 (HM582117), D2/TO/UH16/1974 (HM582111), D2/TO/UH19/1974 (HM582112), D2/TO/UH39/1974 (HM582114), D2/TO/UH44/1974 (HM582115), D2/TO/UH94/1974 (HM582116.1), D2/AS/UH77/1972 (HM582104), D2/AS/UH79/1972 (HM582105), D2/AS/UH85/1972 (HM582106), DENV-2/PR/BID-V3367/1969 (GQ868600), Dengue virus type 2 isolate 1328 (EU056812), DENV-2/MX/BID-V3354/1983 (GQ868588), DENV-2/VE/BID-V3366/1987 (GQ868599), DENV-2/HN/BID-V2945/1984 (FJ898449), DENV-2/MX/BID-V3356/1992 (GQ868590), Dengue virus type 2 isolate IQT-1950 (EU056811), Dengue virus type 2 strain IQT2913 (AF100468.1), Dengue virus type 2 strain IQT1797 (AF100467), Dengue virus type 2 Jamaica/N.1409 (M20558). Full-length nucleotide sequences of DENV2-QR94 and DENV2-PR159 are available at NCBI GenBank under accession numbers JX966379 and JX966380, respectively. Nucleotide sequences were automatically aligned with ClustalW in MEGA5 [] and manually inspected in MEGA5. The phylogeny was inferred under maximum likelihood in MEGA5 using the Tamura-Nei model []. Bootstrapping was conducted in MEGA5 with 1000 replicates. […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Aedes aegypti